ORIGINAL ARTICLE Local representation of global diversity in a cosmopolitan lichen-forming fungal species complex (Rhizoplaca, Ascomycota) Steven D. Leavitt 1,2 *, Fernando Fernandez-Mendoza 3,4 , Sergio Perez-Ortega 5 , Mohammad Sohrabi 6 , Pradeep K. Divakar 7 , Jan Vondrak 8 , H. Thorsten Lumbsch 1 and Larry L. St. Clair 2 1 Department of Botany, Field Museum of Natural History, Chicago, IL, 60605-2496, USA, 2 Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA, 3 Department of Botany and Molecular Evolution, Senckenberg Research Institute, Frankfurt am Main, D-60325, Germany, 4 Biodiversity and Climate Research Center, Frankfurt am Main, D-60325, Germany, 5 Departamento de Biolog ıa Ambiente, Museo Nacional de Ciencias Naturales (CISC), Madrid, E-28006, Spain, 6 Iranian Research Organization for Science and Technology (IROST), Tehran, 15815-115, Iran, 7 Departamento de Biolog ıa Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, 28040, Spain, 8 Institute of Botany, Academy of Sciences, Pr uhonice, CZ-252 43, Czech Republic *Correspondence: Steven D. Leavitt, Department of Biology and M. L. Bean Life Science Museum, 193 MLBM, Brigham Young University, Provo, UT 84602, USA. E-mail: sleavitt@fieldmuseum.org ABSTRACT Aim The relative importance of long-distance dispersal versus vicariance in determining the distribution of lichen-forming fungi remains unresolved. Here, we examined diversity and distributions in a cosmopolitan lichen-forming fun- gal species complex, Rhizoplaca melanophthalma sensu lato (Ascomycota), across a broad, intercontinental geographical distribution. We sought to deter- mine the temporal context of diversification and the impacts of past climatic fluctuations on demographic dynamics within this group. Location Antarctica, Asia, Europe, North America and South America. Methods We obtained molecular sequence data from a total of 240 specimens of R. melanophthalma s.l. collected across five continents. We assessed the monophyly of candidate species using individual gene trees and a tree from a seven-locus concatenated data set. Divergence times and relationships among candidate species were evaluated using a multilocus coalescent-based species tree approach. Speciation probabilities were estimated using the coalescent- based species delimitation program bpp. We also calculated statistics on molec- ular diversity and population demographics for independent lineages. Main conclusions Our analyses of R. melanophthalma s.l. collected from five continents supported the presence of six species-level lineages within this com- plex. Based on current sampling, two of these lineages were found to have broad intercontinental distributions, while the other four were limited to wes- tern North America. Of the six lineages, five were found on a single mountain in the western USA and the sixth occurred no more than 200 km away from this mountain. Our estimates of divergence times suggest that Pleistocene gla- cial cycles played an important role in species diversification within this group. At least three lineages show evidence of recent or ongoing population expan- sion. Keywords BEAST, biogeography, BPP, coalescent, cryptic species, long-distance dispersal, Rhizoplaca melanophthalma, speciation. INTRODUCTION Lichen-forming fungi are obligate symbionts with photoauto- trophic organisms, mainly green algae and/or cyanobacteria. The lichen symbiosis has been highly successful within fungi, especially Ascomycota, with an estimated diversity greater than 28,000 species (L€ ucking et al., 2009a). Lichens play a variety of important ecological roles, including the coloniza- tion of bare soil and rocks (Nascimbene et al., 2009), stabil- ization of soil in arid and semi-arid regions (Belnap & Eldridge, 2001), and contributing to nitrogen influx in some ecosystems (Ponzetti & McCune, 2001; Gavazov et al., 2010; Zhao et al., 2010; Raggio et al., 2012). Additionally, lichens are commonly used as bioindicators to assess environmental disturbance (McCune, 2000; Nimis et al., 2002; Bjerke, 2011; Leavitt & St. Clair, 2011). 1792 http://wileyonlinelibrary.com/journal/jbi ª 2013 Blackwell Publishing Ltd doi:10.1111/jbi.12118 Journal of Biogeography (J. Biogeogr.) (2013) 40, 1792–1806
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ORIGINALARTICLE
Local representation of global diversityin a cosmopolitan lichen-formingfungal species complex (Rhizoplaca,Ascomycota)Steven D. Leavitt1,2*, Fernando Fern�andez-Mendoza3,4, Sergio
P�erez-Ortega5, Mohammad Sohrabi6, Pradeep K. Divakar7, Jan Vondr�ak8,
H. Thorsten Lumbsch1 and Larry L. St. Clair2
1Department of Botany, Field Museum of
Natural History, Chicago, IL, 60605-2496,
USA, 2Department of Biology and M. L. Bean
Life Science Museum, Brigham Young
University, Provo, UT, 84602, USA,3Department of Botany and Molecular
Evolution, Senckenberg Research Institute,
Frankfurt am Main, D-60325, Germany,4Biodiversity and Climate Research Center,
Frankfurt am Main, D-60325, Germany,5Departamento de Biolog�ıa Ambiente, Museo
Nacional de Ciencias Naturales (CISC),
Madrid, E-28006, Spain, 6Iranian Research
Organization for Science and Technology
(IROST), Tehran, 15815-115, Iran,7Departamento de Biolog�ıa Vegetal II,
et al., 2003; Geml et al., 2010). However, the role of long-
distance dispersal versus vicariance in lichen-forming fungi
remains largely unresolved (Printzen et al., 2003; Geml et al.,
2010, 2012; Amo de Paz et al., 2011). While evidence for
intraspecific long-distance dispersal has been documented
(Buschbom, 2007; Geml et al., 2010), assessing diversification
and biogeographical patterns within a temporal context
remains largely unexplored in nearly all groups of lichenized
fungi, with some exceptions (e.g. Ot�alora et al., 2010; Amo
de Paz et al., 2011; S�erusiaux et al., 2011; Leavitt et al.,
2012b,c). This is largely due to a poor fossil record for liche-
nized fungi and uncertainties in the interpretation of the few
known fossil records (Taylor & Berbee, 2006; L€ucking et al.,
2009b; Berbee & Taylor, 2010).
Rhizoplaca melanophthalma (DC.) Leuckert & Poelt is
known from largely disjunct populations on all continents
except Australia (Fig. 1; Egea, 1996; Ryan, 2001; Castello,
2010; Ruprecht et al., 2012). This species occurs on exposed
calcium-poor rock, and ranges in distribution from extre-
mely arid continental habitats to upper montane coniferous
forests and the lower portions of the alpine tundra (McCune,
1987; Ryan, 2001). Analyses of molecular sequence data have
indicated that traditional phenotype-based species circum-
scriptions fail to recognize multiple species-level lineages
within the nominal mycobiont taxon R. melanophthalma
(Leavitt et al., 2011b). The R. melanophthalma species com-
plex (sensu Leavitt et al., 2011b) includes a morphologically
and chemically diverse assemblage of growth forms (McCu-
ne, 1987; Ryan, 2001). Within R. melanophthalma sensu lato
(s.l.), Leavitt et al. (2011b) circumscribed six ‘candidate’ spe-
cies that were supported using multiple lines of evidence
500 Km
Clade 2Rhizoplaca melanophthalma s.l.
Clade 3
Clade 4a
Clade 4b
Clade 4c
Clade 4d
Figure 1 Geographical distribution of Rhizoplaca melanophthalma sensu lato. Filled triangles indicate species records from the GlobalBiodiversity Information Facility database and the Consortium of North American Lichen Herbaria. Coloured circles indicate sampled
geographical populations and colours indicate the proportion of sampled lineages within that geographical population.
Journal of Biogeography 40, 1792–1806ª 2013 Blackwell Publishing Ltd
1793
Biogeography of the Rhizoplaca melanophthalma species complex
from molecular sequence data, including: fixed nucleotide
characters, genealogical exclusivity, Bayesian population clus-
tering and the coalescent-based species delimitation program
bpp (Bayesian Phylogenetics and Phylogeography; Yang &
Rannala, 2010). This last method has recently been shown to
outperform other species-delimitation methods under a vari-
ety of scenarios (Camargo et al., 2012a). Additionally, dis-
tinct species-level lineages in the R. melanophthalma group
are known to occur sympatrically in western North America
with strong evidence of reproductive isolation among lin-
eages, and thus de facto species status (Leavitt et al., 2011b).
Previous studies have suggested that lineages within the
R. melanophthalma complex may be broadly distributed
(Arup & Grube, 2000; Leavitt et al., 2011b). These may
potentially serve as valuable groups for assessing dispersal
capacity and landscape-level genetics in response to changing
climatic conditions. In addition, R. melanophthalma s.l. is
frequently used in air quality biomonitoring studies (Dill-
man, 1996; Ugur et al., 2004) and has been shown to have
pharmaceutical potential for treating drug genotoxicity in
human blood (Geyikoglu et al., 2007). Therefore, accurate
specimen identifications and interpretation of biogeographi-
cal patterns may have important implications for biomoni-
toring and pharmaceutical research.
Currently, molecular species circumscriptions within
R. melanophthalma s.l. have largely been restricted to collec-
tions made in the Intermountain Region of western North
America (Leavitt et al., 2011b). Data from a broader geo-
graphical sampling are essential for understanding distribu-
tion patterns of species-level lineages within this
cosmopolitan species complex. The objectives of this paper
are: (1) to assess the distribution of candidate species-level
lineages within the R. melanophthalma complex within a
broad geographical context; and (2) to estimate divergence
times among species-level lineages using a coalescent-based
multilocus species tree approach. In this study, we analysed
genetic data generated from R. melanophthalma s.l. speci-
mens collected from five continents and report on the distri-
bution patterns of species-level lineages and divergence times
within this complex.
MATERIALS AND METHODS
Taxon sampling
Our sampling focused on Rhizoplaca melanophthalma s.l.
populations from western North America, with supplemen-
tary collections from Antarctica, Central Asia, Europe and
South America. Poelt (1989) suggested that the arid moun-
tain regions in western North America were one of two cen-
tres of distribution for placodioid Lecanora diversity,
including Rhizoplaca. Subsequent studies have supported
nental distributions were identified in two lineages, C2 and
C4b (Fig. 2; Appendix S1). In many cases, specimens of the
broadly distributed lineages (clades C2 and C4b) collected
from geographically distinct regions shared identical ITS
haplotypes (Table 2). In contrast, only specimens collected in
western North America were recovered in clades C3, C4a,
C4c and C4d (Fig. 2, Appendix S1). Of the six species-level
lineages within the R. melanophthalma complex, five were
collected from Thousand Lakes Mountain, UT, USA. The
single lineage not collected on Thousand Lakes Mountain
(C4a) was collected from a site in Juab County, UT, less
than 200 km away.
Individual gene trees are shown in Fig. 3. Monophyly and
bootstrap support for all clades is summarized for all single-
gene topologies in Table 3. Despite the strong support for
many lineages in individual gene trees, well-supported rela-
tionships among species were largely discordant among gene
topologies. In the total-evidence analysis, the partitioned ML
analysis of the combined ribosomal and protein-coding
genes is presented in Fig. 4. The concatenated ML topology
is characterized by well-supported monophyletic lineages
corresponding to candidate lineages circumscribed in Leavitt
et al. (2011b), with the exception of lineage C4d
(BS < 50%).
Journal of Biogeography 40, 1792–1806ª 2013 Blackwell Publishing Ltd
1796
S. D. Leavitt et al.
Coalescent-based species tree and divergence
estimates
Large effective sample sizes (ESS > 200) were observed for
all parameters in the *beast analyses. The time-calibrated
maximum clade credibility chronogram from the multi-locus
species tree analysis is shown in Fig. 5. The substitution rates
of the seven sampled loci, estimated under a relaxed clock,
are reported in Table 4. The initial split between Lecanora
novomexicana and the R. melanophthalma complex was
Table 1 Genetic variability of sampled markers in the Rhizoplaca melanophthalma species complex, including the number of specimens
(n) and number of unique haplotypes (in parentheses), alignment length (bp), number of variable sites, number of parsimony-informative (PI) sites for each sampled locus, and the model of evolution identified for each locus using the Akaike information
criterion in jModelTest. Collections were made in Antarctica, Asia, Europe and North and South America.
Locus n Aligned length No. of variable sites No. of PI sites Model selected
Figure 2 Cartoon representation of the maximum likelihood ITS topology obtained from 240 Rhizoplaca melanophthalma sensu lato
specimens. Values at each node indicate non-parametric bootstrap support; only support values > 50% are indicated. Tip labelsrepresent the six candidate species-level lineages; the vagrant taxa Rhizoplaca haydenii and R. idahoensis are combined into a single clade
‘vagrant Rhizoplaca spp.’. The country of origin for all specimens recovered within each clade is indicated below the tip label.
Journal of Biogeography 40, 1792–1806ª 2013 Blackwell Publishing Ltd
1797
Biogeography of the Rhizoplaca melanophthalma species complex
estimated to have occurred during the Miocene, c. 8.7 Ma
(95% highest posterior density, HPD: 5.2–12.7 Ma), and the
initial radiation of the R. melanophthalma group during the
Pliocene, c. 4.4 Ma (95% HPD: 2.7–6.3 Ma). Divergence esti-
mates indicate that the majority of the diversification leading
to extant species, including the vagrant species, occurred
during the Pleistocene (Fig. 5).
Speciation probabilities
Speciation probabilities (SP) estimated using the program bpp
are shown in Fig. 5. With the exception of the split between
the two vagrant species (R. haydenii and R. idahoensis),
high speciation probabilities (SP � 0.95) were estimated at
all nodes, using both the default prior gamma distributions
for h [G(2, 1000)] and τ0 [G(2, 1000)] and a more moderate
combination of these priors – G(2, 100) and G(2, 2000) for
h and τ0, respectively. Under the most conservative combina-
tion of priors – h, G(2, 10) and G(2, 2000) for h and τ0,respectively – speciation probabilities match those supported
using the default priors, with the exception of lower proba-
bilities for a split between C4d and C4c (SP < 0.50).
Molecular diversity and population demographics
Genetic diversity indices (Hd, S and p) for species within the
R. melanophthalma species complex are summarized in
Table 5. Tajima’s D and Fu’s FS statistics were significant
(P < 0.05) and negative for lineages C2, C4b and C4d
(Table 5). No tests were carried out for clades C4a and C4c
or the vagrant species R. haydenii and R. idahoensis, because
of their small sample sizes.
DISCUSSION
Our analyses of specimens of R. melanophthalma s.l. col-
lected from five continents support the presence of the six
species-level lineages within this nominal species identified
previously from collections made in western North America
(Leavitt et al., 2011b). Despite the increased sampling in this
study, including populations from Antarctica, Central Asia,
Europe and South America, we did not identify any addi-
tional species-level lineages within this complex. Two of the
six lineages were found to have broad intercontinental distri-
butions (clades C2 and C4b), and in many cases individuals
shared identical ITS haplotypes among geographically dis-
junct populations (Table 2). Based on the current sampling,
the other four lineages were found exclusively in western
North America. Surprisingly, of the six known species-level
lineages within R. melanophthalma s.l., five are found on a
single mountain in the western USA and the sixth is known
to occur at a distance of no greater than 200 km from that
site. Our results highlight a striking case in which the known
species diversity in a cosmopolitan species complex is repre-
sented in a geographically local region.
Specific factors determining distribution patterns for the
various distinct lineages within the R. melanophthalma spe-
cies complex remain unclear. However, the broad geographi-
cal distributions of clades C2 and C4b and population
demographic statistics indicate that these two lineages are
likely to have experienced recent population growth
(Table 5). In contrast to the broad intercontinental distribu-
tion of clades C2 and C4b, clades C3, C4a, C4c and C4d
appear to be restricted to western North America. Of these
western North American lineages, one clade, C4d, is com-
monly found on rocks, from lower-elevation pinyon–juniper
woodlands to montane coniferous forests and lower alpine
tundra. A second lineage, C3, appears to be restricted to sub-
alpine habitats in the south-western USA, where it is locally
common. The remaining two lineages known only from wes-
tern North America occur more rarely throughout lower-
elevation habitats in western North America (see Leavitt
et al., 2013b). Given the apparent dispersal capacity of other
closely related lineages in this species complex (i.e. clades C2
and C4b), it seems unlikely that geographical distributions
are restricted to North America due to limited dispersal
capacity in these lineages. Although the effective dispersal of
lichen-forming fungal species by spores is limited by the
availability of appropriate substrata and other ecogeographi-
cal factors, other unrecognized dispersal limitations or estab-
lishment barriers appear to have limited the distribution of
some lineages of R. melanophthalma s.l. Alternatively, it has
also been proposed that competition for symbiotic partners
may be a major driver of diversity in mutualistic relation-
ships (Bruns, 1995; O’Brien et al., 2009), and investigating
competition for symbionts may provide insights into mecha-
nisms that may influence distributions.
While previous studies have suggested that Pleistocene gla-
cial cycles played only a minor role in diversification accom-
panied by speciation in lichen-forming fungi (Ot�alora et al.,
2010; Amo de Paz et al., 2011, 2012; Leavitt et al., 2012a,b,c),
the divergence times estimated in this study suggest that the
majority of the speciation events in the R. melanophthalma
complex occurred during the Pleistocene (Fig. 5). The rela-
tively recent diversification history for the R. melanophthalma
group, its apparent centre of diversity in western North
Table 2 Shared ITS haplotypes across intercontinental
populations of Rhizoplaca melanophthalma sensu lato. The ‘DNAID no.’ refers to an individual representing the shared ITS
haplotype.
DNA ID no. Geographical origin
R. aff. melanophthalma ‘C2’
720 USA, China, Chile, Spain, Switzerland
4610 USA & Spain
5186 Chile & Iran
China_1985 Chile, China, Spain
Spain_1983 Spain & USA
R. aff. melanophthalma ‘C4b’
551 Chile, Spain, USA
6028 China, Chile, Kyrgyzstan
Chile_6838 Chile & China
Journal of Biogeography 40, 1792–1806ª 2013 Blackwell Publishing Ltd
1798
S. D. Leavitt et al.
0.009 substitutions/site
‘C4d’ 658
‘C4c’ 556
‘C2’ 6724‘C2’ 6725
Lecanora novomexicana 731
‘C2’ 6742
‘C4d’ 542
‘C4c’ 554
‘C4b’ 635‘C4b’ 664
‘C4d’ 713
‘C4d’ 639
‘C4b’ 6743
‘R. idahoensis’ 103
‘C2’ 5170
‘C2’ 677
‘C3’ 589
‘C2’ 660‘C2’ 563
‘R. haydenii’ 684
‘C2’ 612
‘C4d’ 4285
L. novomexicana 733
‘C4c’ 669
‘C3’ 572‘C3’ 586
‘C2’ 587‘C3’ 652
‘C2’ 6030
‘C3’ 571
‘C4a’ 695
L. novomexicana 732
‘C2’ 5178
‘C2’ 5174
‘C4b’ 551
‘C4d’ 641
‘C4a’ 714‘C4a’ 706
98
95
78
100
71
99
98
54
100
95
100
97
89
85
95
77 67
97
0.003 substitutions/site
‘C3’ 586
‘C2’ 612
‘C4d’ 639
‘C2’ 6030
‘C2’ 6742
‘C4d’ 713
‘C2’ 587
‘C2’ 660
‘C2’ 677
‘C4a’ 714
‘C3’ 572
‘C4b’ 551
‘C4a’ 706
‘C2’ 563
‘C4d’ 4285
R. haydenii 684‘C2’ 5174
‘C4c’ 554
‘C3’ 571
‘C2’ 5178
‘C4c’ 4616
‘C4b’ 664
‘C4d’ 641
‘C2’ 5167
‘C4d’ 658
‘C4c’ 556
‘C3’ 652
‘C4c’ 669
‘C4b’ 6743
‘C2’ 6725
‘C4b’ 635
‘C4d’ 542
‘C4a’ 695
R. idahoensis 103
‘C2’ 5170
‘C2’ 6724
‘C3’ 589
100
100
92
99
86
100
96
93
10097
96
99
91
0.004 substitutions/site
‘C4c’ 556
‘C2’ 6724
‘C4a’ 706
‘C4b’ 6743
‘C2’ 5170
Lecanora novomexicana 731
‘C2’ 612
‘C4d’ 639
‘C4b’ 664
‘C4a’ 714
‘C2’ 6030
R. idahoensis 103
‘C4d’ 641
‘C2’ 660
‘C4d’ 658
‘C3’ 652
‘C2’ 677
R. haydenii 684
‘C4d’ 4285
‘C4c’ 4616
‘C2’ 6725
‘C2’ 5174
‘C4b’ 551
‘C3’ 589
‘C4d’ 713
‘C4c’ 669
‘C2’ 563
‘C4a’ 695
‘C3’ 571‘C3’ 586
L. novomexicana 733
‘C2’ 587
‘C2’ 5178
L. novomexicana 732
‘C4d’ 542
‘C4c’ 554
‘C3’ 572
‘C4b’ 635
‘C2’ 6742
74
89
100
100
89
99
8791
8296 1
7692
95
78
100
0.003 substitutions/site
Lecanora novomexicana 733
‘C3’ 589
‘C4d’ 639‘C4a’ 706
‘C4c’ 4616
‘C2’ 5174
‘C2’ 660
‘C3’ 572
‘C4d’ 641
‘C2’ 6030‘C2’ 612
‘C4b’ 635
‘C4d’ 4285
‘C4a’ 695
‘C2’ 677
‘C4c’ 669
‘C4d’ 542
‘C2’ 6724 ‘C2’ 587
‘C3’ 571
‘C4a’ 714
‘C4c’ 554
‘C4d’ 658
L. novomexicana 732
‘C2’ 563 ‘C2’ 6725
‘C2’ 5178
‘C3’ 586
‘C2’ 5167
R. idahoensis 103
‘C2’ 5170
‘C4b’ 6743
‘C4d’ 713
‘C4b’ 551
R. haydenii 684
‘C4c’ 556
‘C2’ 6742
‘C4b’ 664
L. novomexicana 731
100
100
98
100
100
100
100
100
100
100
100
100
100
(a) (b)IGS beta-tubulin
(d) MCM7
RPB2
0.004 substitutions/site
‘C2’ 5170‘C2’ 6725
‘C4c’ 554
Lecanora novomexicana 731
‘C4b’ 664
‘C4d’ 658
‘C3’ 571
‘C2’ 563
‘C2’ 677
‘C4b’ 635‘C4b’ 551
L. novomexicana 733 L. novomexicana 732
‘C4d’ 639‘C4d’ 641‘C4d’ 713
‘C4b’ 6743
‘C2’ 587
‘C4d’ 4285
‘C2’ 5174‘C2’ 612
‘C3’ 586
R. idahoensis 103
‘C4a’ 695
‘C2’ 6724
‘C4c’ 556
‘C4c’ 669
R. haydenii 684
‘C2’ 5178
‘C3’ 572
‘C4c’ 4616
‘C3’ 652
‘C2’ 6742‘C2’ 660
‘C2’ 6030
‘C4a’ 714‘C3’ 589
‘C4d’ 552‘C4a’ 706
100
82
92
100
100 95
100
100
9598
8
(e) (f)RPB
0.007 substitutions/site
‘C4c’ 4616‘C4d’ 713
‘C4c’ 554
Lecanora novomexicana 732
‘C2’ 587‘C2’ 6725
‘C4c’ 556
‘C4b’ 635
‘C4d’ 641
‘C2’ 6742
‘C3’ 571
‘C2’ 660
‘C4b’ 551
‘C2’ 563
‘C4a’ 714
R. haydenii 103
‘C4b’ 664
‘C4d’ 639
‘C2’ 5174
‘C3’ 652
‘C4d’ 542
‘C3’ 586
‘C2’ 612
‘C4c’ 669
‘C2’ 6724
‘C3’ 589
‘C2’ 5167
‘C4a’ 706
‘C4a’ 695
‘C2’ 677
‘C3’ 572R. haydenii 684
‘C4b’ 6743
‘C2’ 5178 L. novomexicana 733
‘C2’ 5170
L. novomexicana 731
‘C4d’ 658
99
100
78
77
7
51
100
98
51
81
(c) EF1
Lecanora novomexicana 731L. novomexicana 733
L. novomexicana 732
Clade 2
Clade 3
Clade 4a
Clade 4b
Clade 4c
Clade 4d
Figure 3 Individual maximum likelihood gene trees (a, IGS; b, b-tubulin; c, EF1; d, MCM7; e, RPB1; f, RPB2) inferred from 38–40specimens representing all candidate species-level lineages in the Rhizoplaca melanophthalma species complex using the program
RAxML. The ITS topology is shown in Fig. 1 and Appendix S1.
Journal of Biogeography 40, 1792–1806ª 2013 Blackwell Publishing Ltd
1799
Biogeography of the Rhizoplaca melanophthalma species complex
0.0050 substitutions/site
Lecanora novomexicana 732
695542
713
554
677
6030
587
706
669
5178
664
551
4285
6724
639
586
R. haydenii 684
556
589572
4616
5174
714
6743
571
660
658641
5167
5170
Lecanora novomexicana 733
612
R. idahoensis 103
635
6742
Lecanora novomexicana 731
6725
652
563
100
74
100
100
91
99
60
50
100
100
95
60
100
94
66
100
98
95
90
100
100
73
88
58
79
93
98
84
R. aff. melanophthalma ‘C4b’
R. aff. melanophthalma ‘C4c’
R. aff. melanophthalma ‘C4a’
R. aff. melanophthalma ‘C4d’
R. aff. melanophthalma ‘C2’
R. aff. melanophthalma ‘C3’
84
Figure 4 Relationships among 40 specimens representing all candidate species-level lineages in the Rhizoplaca melanophthalma species
complex inferred from a maximum likelihood analysis of nuclear ribosomal and protein-coding DNA sequence data (ITS, IGS,b-tubulin, EF1, MCM7, RPB1 and RPB2 markers, 4179 total base pairs). Values at each node indicate non-parametric bootstrap support
(percent); only support values > 50% are indicated.
Table 3 Summary of lineage monophyly across the seven sampled loci and a concatenated gene tree for the Rhizoplaca melanophthalma
species complex. Values indicate nonparametric-bootstrap support estimated in RAxML 7.2.8, and dashes indicate instances where thespecific lineage was not recovered as monophyletic. Collections were made in Antarctica, Asia, Europe and North and South America.
ITS IGS b-tubulin EF1 MCM7 RPB1 RPB2 combined
Lineage C2 91% 77% — — 96% 100% 100% 100%
Lineage C3 100% 98% 100% — 99% 100% 98% 100%
Lineage C4a 99% 97% — — — — — 100%
Lineage C4b 67% < 50% 99% — — 100% 100% 100%
Lineage C4c 66% 95% — — — — — 84%
Lineage C4d 94% — — — — — — < 50%
Figure 5 Time-calibrated maximum clade credibility tree for the Rhizoplaca melanophthalma species complex. The chronogram wasestimated from a multilocus data set (ITS, IGS, b-tubulin, EF1, MCM7, RPB1 and RPB2 markers) within a coalescence-based framework
in *beast. The divergence times correspond to the mean posterior estimate of their age, in millions of years. The bars indicate the 95%highest posterior density (HPD) interval for the divergence times estimates. Values above branches indicate posterior probability; only
values > 0.50 are presented. The three values below branches indicate speciation probabilities estimated using the program bpp 2.1 usingdefault, moderate and conservative priors for the gamma distribution of h and τ0 (see text for details).
Journal of Biogeography 40, 1792–1806ª 2013 Blackwell Publishing Ltd
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S. D. Leavitt et al.
America, and recent population expansions for at least three
of the six lineages (Table 5) support the idea that diversifica-
tion may have occurred in western North America during the
Pleistocene with subsequent long-distance dispersal resulting
in the contemporary distribution patterns.
Large areas of North America were subject to global cool-
ing, aridification and major glaciation events during the